Package picard.analysis
Class CollectOxoGMetrics
- java.lang.Object
-
- picard.cmdline.CommandLineProgram
-
- picard.analysis.CollectOxoGMetrics
-
@DocumentedFeature public class CollectOxoGMetrics extends CommandLineProgram
Class for trying to quantify the CpCG->CpCA error rate.
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectOxoGMetrics.CpcgMetrics
Metrics class for outputs.
-
Field Summary
Fields Modifier and Type Field Description int
CONTEXT_SIZE
Set<String>
CONTEXTS
File
DB_SNP
boolean
INCLUDE_NON_PF_READS
File
INPUT
File
INTERVALS
int
MAXIMUM_INSERT_SIZE
int
MINIMUM_INSERT_SIZE
int
MINIMUM_MAPPING_QUALITY
int
MINIMUM_QUALITY_SCORE
File
OUTPUT
int
STOP_AFTER
boolean
USE_OQ
-
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
-
Constructor Summary
Constructors Constructor Description CollectOxoGMetrics()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.protected boolean
requiresReference()
-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
-
-
-
-
Field Detail
-
INPUT
@Argument(shortName="I", doc="Input SAM/BAM/CRAM file for analysis.") public File INPUT
-
OUTPUT
@Argument(shortName="O", doc="Location of output metrics file to write.") public File OUTPUT
-
INTERVALS
@Argument(doc="An optional list of intervals to restrict analysis to.", optional=true) public File INTERVALS
-
DB_SNP
@Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.", optional=true) public File DB_SNP
-
MINIMUM_QUALITY_SCORE
@Argument(shortName="Q", doc="The minimum base quality score for a base to be included in analysis.") public int MINIMUM_QUALITY_SCORE
-
MINIMUM_MAPPING_QUALITY
@Argument(shortName="MQ", doc="The minimum mapping quality score for a base to be included in analysis.") public int MINIMUM_MAPPING_QUALITY
-
MINIMUM_INSERT_SIZE
@Argument(shortName="MIN_INS", doc="The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.") public int MINIMUM_INSERT_SIZE
-
MAXIMUM_INSERT_SIZE
@Argument(shortName="MAX_INS", doc="The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.") public int MAXIMUM_INSERT_SIZE
-
INCLUDE_NON_PF_READS
@Argument(shortName="NON_PF", doc="Whether or not to include non-PF reads.") public boolean INCLUDE_NON_PF_READS
-
USE_OQ
@Argument(doc="When available, use original quality scores for filtering.") public boolean USE_OQ
-
CONTEXT_SIZE
@Argument(doc="The number of context bases to include on each side of the assayed G/C base.") public int CONTEXT_SIZE
-
CONTEXTS
@Argument(doc="The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.", optional=true) public Set<String> CONTEXTS
-
STOP_AFTER
@Argument(doc="For debugging purposes: stop after visiting this many sites with at least 1X coverage.") public int STOP_AFTER
-
-
Method Detail
-
requiresReference
protected boolean requiresReference()
- Overrides:
requiresReference
in classCommandLineProgram
-
customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
-
doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
-
-